{"id":{"repo_id":"helsinki","oai_identifier":"oai:helda.helsinki.fi:10138/306755"},"canonical_url":"https://search.dev.ndltd.org/etd/helsinki/oai:helda.helsinki.fi:10138/306755","repository":{"repo_id":"helsinki","name":"University of Helsinki","base_url":"https://helda.helsinki.fi/server/oai/request"},"display":{"title":"Protomyces Comparative Genomics and Modulation of Arabidopsis Immunity","abstract":"The plant phyllosphere environment offers a habitat for multiple kinds of microbes, including bacteria, fungi, yeast, etc. Microbes can be beneficial, pathogenic, or mostly neutral to plants. Increasingly the interaction patterns and related plant immunity signaling pathways against bacteria and filamentous fungi have been extensively studied. However, the interaction between plants and yeast or yeast-like fungi is largely unclear. Phyllosphere yeast-like fungi from wild Arabidopsis were isolated and characterized in this study. Around a hundred yeast isolates, including ascomycete Protomyces species, were identified and cultured. Protomyces species have been described as pathogens of plants in the Umbelliferae and Compositae families, however, with questionable phylogeny and little genomic information. We isolated and investigated the interaction of a strain Protomyces sp. SC29 (SC29) with Arabidopsis. SC29 can persist in the Arabidopsis phylloplane, and activate Arabidopsis immune responses with MAPKs (mitogen-activated protein kinases) activation and upregulation of salicylic acid signaling and camalexin biosynthesis marker genes. Additionally, indolic compounds produced by Protomyces species are able to activate plant auxin responses. The genomes of SC29 and all currently available Protomyces species were sequenced, assembled, and annotated. Comparative genomic analysis revealed genomic characters of SC29 related to adaptation to the phyllosphere environment. Genomic insights into the pathogenesis of Protomyces species were also discovered. The phylogenetic relationships of both the genus Protomyces and the subphylum Taphrinomycotina were re-constructed with genome-wide single-copy protein sequences. Small secreted proteins from the genomes of Protomyces spp. were analyzed as candidate effectors. Physiological, phylogenetic, and genomic evidence supported SC29 to be a novel species distinct from currently accepted Protomyces species. Thus, the study of SC29 and its interaction with Arabidopsis represents a new model system for the exploration of the genetics of plant interactions with phyllosphere resident yeasts.","abstract_html":"The plant phyllosphere environment offers a habitat for multiple kinds of microbes, including bacteria, fungi, yeast, etc. Microbes can be beneficial, pathogenic, or mostly neutral to plants. Increasingly the interaction patterns and related plant immunity signaling pathways against bacteria and filamentous fungi have been extensively studied. However, the interaction between plants and yeast or yeast-like fungi is largely unclear. Phyllosphere yeast-like fungi from wild Arabidopsis were isolated and characterized in this study. Around a hundred yeast isolates, including ascomycete Protomyces species, were identified and cultured. Protomyces species have been described as pathogens of plants in the Umbelliferae and Compositae families, however, with questionable phylogeny and little genomic information. We isolated and investigated the interaction of a strain Protomyces sp. SC29 (SC29) with Arabidopsis. SC29 can persist in the Arabidopsis phylloplane, and activate Arabidopsis immune responses with MAPKs (mitogen-activated protein kinases) activation and upregulation of salicylic acid signaling and camalexin biosynthesis marker genes. Additionally, indolic compounds produced by Protomyces species are able to activate plant auxin responses. The genomes of SC29 and all currently available Protomyces species were sequenced, assembled, and annotated. Comparative genomic analysis revealed genomic characters of SC29 related to adaptation to the phyllosphere environment. Genomic insights into the pathogenesis of Protomyces species were also discovered. The phylogenetic relationships of both the genus Protomyces and the subphylum Taphrinomycotina were re-constructed with genome-wide single-copy protein sequences. Small secreted proteins from the genomes of Protomyces spp. were analyzed as candidate effectors. Physiological, phylogenetic, and genomic evidence supported SC29 to be a novel species distinct from currently accepted Protomyces species. Thus, the study of SC29 and its interaction with Arabidopsis represents a new model system for the exploration of the genetics of plant interactions with phyllosphere resident yeasts.","abstract_has_math":false,"creators":["Wang, Kai"],"institution":"Helsingin yliopisto","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-11-29","date_published":"2019-11-29","updated_at":"2026-08-21T22:21:56Z","subjects":["Plant Sciences"],"languages":["eng"],"rights":["Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.","This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.","Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/10138/306755","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"source_record":{"url":"https://helda.helsinki.fi/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Ahelda.helsinki.fi%3A10138%2F306755","prefix":"dim"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Wang, Kai"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2019-11-05T15:03:22Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2019-11-19","2019-11-05T15:03:22Z"]},{"key":"dc:date.issued","label":"Date","values":["2019-11-29"]},{"key":"dc:publisher","label":"Institution","values":["Helsingin yliopisto","Helsingfors universitet","University of Helsinki"]},{"key":"dc:type.dcmitype","label":"Dc Type Dcmitype","values":["Text"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Plant Sciences"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.","This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.","Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/10138/306755"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The plant phyllosphere environment offers a habitat for multiple kinds of microbes, including bacteria, fungi, yeast, etc. Microbes can be beneficial, pathogenic, or mostly neutral to plants. Increasingly the interaction patterns and related plant immunity signaling pathways against bacteria and filamentous fungi have been extensively studied. However, the interaction between plants and yeast or yeast-like fungi is largely unclear. Phyllosphere yeast-like fungi from wild Arabidopsis were isolated and characterized in this study. Around a hundred yeast isolates, including ascomycete Protomyces species, were identified and cultured. Protomyces species have been described as pathogens of plants in the Umbelliferae and Compositae families, however, with questionable phylogeny and little genomic information. We isolated and investigated the interaction of a strain Protomyces sp. SC29 (SC29) with Arabidopsis. SC29 can persist in the Arabidopsis phylloplane, and activate Arabidopsis immune responses with MAPKs (mitogen-activated protein kinases) activation and upregulation of salicylic acid signaling and camalexin biosynthesis marker genes. Additionally, indolic compounds produced by Protomyces species are able to activate plant auxin responses. The genomes of SC29 and all currently available Protomyces species were sequenced, assembled, and annotated. Comparative genomic analysis revealed genomic characters of SC29 related to adaptation to the phyllosphere environment. Genomic insights into the pathogenesis of Protomyces species were also discovered. The phylogenetic relationships of both the genus Protomyces and the subphylum Taphrinomycotina were re-constructed with genome-wide single-copy protein sequences. Small secreted proteins from the genomes of Protomyces spp. were analyzed as candidate effectors. Physiological, phylogenetic, and genomic evidence supported SC29 to be a novel species distinct from currently accepted Protomyces species. Thus, the study of SC29 and its interaction with Arabidopsis represents a new model system for the exploration of the genetics of plant interactions with phyllosphere resident yeasts.","Kasvin fyllosfääri tarjoaa elinympäristön monenlaisille mikrobeille, kuten bakteereille, sienille ja hiivoille. Mikrobit voivat olla hyödyllisiä, patogeenisiä tai lähinnä neutraaleja kasveille. Kasvien vuorovaikutuskuvioita mikrobien kanssa ja siihen liittyviä kasvien immuniteettisignaloinnin polkuja bakteereja sekä rihmasieniä vastaan on tutkittu enenevässä määrin, mutta vuorovaikutus kasvien ja hiivojen tai hiivan kaltaisten sienien välillä on kuitenkin suurelta osin epäselvää. Tässä tutkimuksessa eristettiin ja karakterisoitiin hiivan kaltaisia sieniä villinä kasvaneiden lituruohojen fyllosfääreistä. Noin sata hiivaisolaattia, sisältäen kotelosieniin kuuluvia Protomyces-lajeja, tunnistettiin ja viljeltiin. Protomyces-lajeja on kuvailtu patogeenisiksi sarjakukkais- (Umbelliferae) ja mykerökukkaiskasveille (Compositae), mutta tähän liittyvä fylogenetiikka on ollut kyseenalaista ja genomitietoa on ollut vähän. Eristimme kannan Protomyces sp. SC29 (SC29) ja tutkimme sen vuorovaikutusta lituruohon kanssa. SC29 kykenee selviytymään lituruohon lehdistön pinnalla ja se aktivoi lituruohon immuunivasteita mitogeeniaktivoituvia proteiinikinaaseja aktivoimalla sekä sääntelemällä ylös salisyylihapposignalointia ja kamaleksiinin biosynteesin markkerigeenejä. Lisäksi, Protomyces-lajien tuottamat indoliyhdisteet kykenevät aktivoimaan kasvin auksiinivasteita. SC29:n ja kaikkien tällä hetkellä saatavilla olevien Protomyces-lajien genomit sekvensoitiin, koottiin ja annotoitiin. Vertaileva genomianalytiikka paljasti SC29:stä genomisia piirteitä, jotka liittyvät sopeutumiseen fyllosfääriympäristöön. Myös genomin yhteyksiä Protomyces-lajien patogeenisyyteen löydettiin. Sekä Protomyces-suvun että Taphrinomycotina-alajakson fylogeneettiset suhteet estimoitiin käyttäen proteiinisekvenssejä, joita löytyi vain yhtenä kopiona koko genomista. Protomyces-lajien genomeista tunnistettuja pieniä erittyviä proteiineja analysoitiin mahdollisina efektoreina. Fysiologinen, fylogeneettinen ja genominen aineisto antoi tukea sille, että SC29 olisi uusi laji ja erillinen tällä hetkellä hyväksytyistä Protomyces-lajeista. Tämä SC29:ään ja sen interaktioon lituruohon kanssa kohdistettu tutkimus tarjoaa uuden mallijärjestelmän, jolla voidaan tutkia kasvin ja fyllosfääriä asuttavien hiivojen välillä tapahtuvien vuorovaikutusten genetiikkaa."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Protomyces Comparative Genomics and Modulation of Arabidopsis Immunity"]}]}],"canonical_facts":{"dc:creator":["Wang, Kai"],"dc:date.accessioned":["2019-11-05T15:03:22Z"],"dc:date.available":["2019-11-19","2019-11-05T15:03:22Z"],"dc:date.issued":["2019-11-29"],"dc:description.abstract":["The plant phyllosphere environment offers a habitat for multiple kinds of microbes, including bacteria, fungi, yeast, etc. Microbes can be beneficial, pathogenic, or mostly neutral to plants. Increasingly the interaction patterns and related plant immunity signaling pathways against bacteria and filamentous fungi have been extensively studied. However, the interaction between plants and yeast or yeast-like fungi is largely unclear. Phyllosphere yeast-like fungi from wild Arabidopsis were isolated and characterized in this study. Around a hundred yeast isolates, including ascomycete Protomyces species, were identified and cultured. Protomyces species have been described as pathogens of plants in the Umbelliferae and Compositae families, however, with questionable phylogeny and little genomic information. We isolated and investigated the interaction of a strain Protomyces sp. SC29 (SC29) with Arabidopsis. SC29 can persist in the Arabidopsis phylloplane, and activate Arabidopsis immune responses with MAPKs (mitogen-activated protein kinases) activation and upregulation of salicylic acid signaling and camalexin biosynthesis marker genes. Additionally, indolic compounds produced by Protomyces species are able to activate plant auxin responses. The genomes of SC29 and all currently available Protomyces species were sequenced, assembled, and annotated. Comparative genomic analysis revealed genomic characters of SC29 related to adaptation to the phyllosphere environment. Genomic insights into the pathogenesis of Protomyces species were also discovered. The phylogenetic relationships of both the genus Protomyces and the subphylum Taphrinomycotina were re-constructed with genome-wide single-copy protein sequences. Small secreted proteins from the genomes of Protomyces spp. were analyzed as candidate effectors. Physiological, phylogenetic, and genomic evidence supported SC29 to be a novel species distinct from currently accepted Protomyces species. Thus, the study of SC29 and its interaction with Arabidopsis represents a new model system for the exploration of the genetics of plant interactions with phyllosphere resident yeasts.","Kasvin fyllosfääri tarjoaa elinympäristön monenlaisille mikrobeille, kuten bakteereille, sienille ja hiivoille. Mikrobit voivat olla hyödyllisiä, patogeenisiä tai lähinnä neutraaleja kasveille. Kasvien vuorovaikutuskuvioita mikrobien kanssa ja siihen liittyviä kasvien immuniteettisignaloinnin polkuja bakteereja sekä rihmasieniä vastaan on tutkittu enenevässä määrin, mutta vuorovaikutus kasvien ja hiivojen tai hiivan kaltaisten sienien välillä on kuitenkin suurelta osin epäselvää. Tässä tutkimuksessa eristettiin ja karakterisoitiin hiivan kaltaisia sieniä villinä kasvaneiden lituruohojen fyllosfääreistä. Noin sata hiivaisolaattia, sisältäen kotelosieniin kuuluvia Protomyces-lajeja, tunnistettiin ja viljeltiin. Protomyces-lajeja on kuvailtu patogeenisiksi sarjakukkais- (Umbelliferae) ja mykerökukkaiskasveille (Compositae), mutta tähän liittyvä fylogenetiikka on ollut kyseenalaista ja genomitietoa on ollut vähän. Eristimme kannan Protomyces sp. SC29 (SC29) ja tutkimme sen vuorovaikutusta lituruohon kanssa. SC29 kykenee selviytymään lituruohon lehdistön pinnalla ja se aktivoi lituruohon immuunivasteita mitogeeniaktivoituvia proteiinikinaaseja aktivoimalla sekä sääntelemällä ylös salisyylihapposignalointia ja kamaleksiinin biosynteesin markkerigeenejä. Lisäksi, Protomyces-lajien tuottamat indoliyhdisteet kykenevät aktivoimaan kasvin auksiinivasteita. SC29:n ja kaikkien tällä hetkellä saatavilla olevien Protomyces-lajien genomit sekvensoitiin, koottiin ja annotoitiin. Vertaileva genomianalytiikka paljasti SC29:stä genomisia piirteitä, jotka liittyvät sopeutumiseen fyllosfääriympäristöön. Myös genomin yhteyksiä Protomyces-lajien patogeenisyyteen löydettiin. Sekä Protomyces-suvun että Taphrinomycotina-alajakson fylogeneettiset suhteet estimoitiin käyttäen proteiinisekvenssejä, joita löytyi vain yhtenä kopiona koko genomista. Protomyces-lajien genomeista tunnistettuja pieniä erittyviä proteiineja analysoitiin mahdollisina efektoreina. Fysiologinen, fylogeneettinen ja genominen aineisto antoi tukea sille, että SC29 olisi uusi laji ja erillinen tällä hetkellä hyväksytyistä Protomyces-lajeista. Tämä SC29:ään ja sen interaktioon lituruohon kanssa kohdistettu tutkimus tarjoaa uuden mallijärjestelmän, jolla voidaan tutkia kasvin ja fyllosfääriä asuttavien hiivojen välillä tapahtuvien vuorovaikutusten genetiikkaa."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["http://hdl.handle.net/10138/306755"],"dc:language.iso":["eng"],"dc:publisher":["Helsingin yliopisto","Helsingfors universitet","University of Helsinki"],"dc:rights":["Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.","This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.","Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden."],"dc:subject":["Plant Sciences"],"dc:title":["Protomyces Comparative Genomics and Modulation of Arabidopsis Immunity"],"dc:type.dcmitype":["Text"]},"updated_at":"2026-08-21T22:21:56Z"}